The Buccaneers were hoping to start their Champions League campaign on a winning note having defeated arch-rivals Kaizer Chiefs in their previous encounter last weekend.
Milutin 'Micho' Sredojevic made nine changes to the team that faced Amakhosi with the experienced Mpho Makola captaining the team in the absence of Happy Jele.
Stars, who qualified for the competition after winning this year's Seychelles League Cup, were keen to cause a major upset by defeating the 1995 Champions League winners.
They had to dig deep in order to secure a stunning win in South Africa having been thumped 6-0 by PSL side Bidvest Wits in the 2016 Caf Confederation Cup preliminary round second-leg clash in Johannesburg.
As one might have expected Buccaneers dominated the match from the start - creating chance after chance with the visitors forced to sit back and defend.
Rome Barra was the busier of the two goalkeepers as he pulled off great saves to deny Caio Marcelo, Augustine Mulenga and Thabo Qalinge in the opening stages of the game.
The deadlock was surprisingly broken by Stars against the run of play after Kudakwashe Mahachi had given away possession in the middle of the park.
The hosts were punished by Mario Ravo, who fired past on-rushing Mabokgwane to hand Stars a 1-0 lead following a quick counter-attack by the away side in the 17th minute.
However, the lead only lasted for six minutes as Thabo Qalinge scored from close range to make it 1-1 after Mahachi's shot was parried by Seychelles international Barra.
The momentum was with Pirates with the half-time break and they took the lead through Mulenga, who scored to make it 2-1 to Pirates following a good move in the 37th minute.
Pirates kept pushing for more goals and they managed to score through Makola, who scored with beautiful curling free-kick to make it 3-1 to the hosts just before the half-time break.
The goals did not come as a surprise as the Buccaneers had scored the majority of their goals (50%) between the 15th minute and 45th minute in PSL matches this season.
The score was 3-1 to Pirates following a first half which was dominated by the home side.
The Buccaneers continued to boss possession after the restart with Makola and Linda Mntambo pulling the strings from the middle of the park for the hosts.
However, the Soweto giants were wasteful in front of goal with the likes of Mntambo, Marcelo, Mahachi guilty of missing the target with the visitors' defence exposed.
Sredojevic introduced Zambian marksman Justin Shonga, who had netted against Chiefs last weekend, as the hosts looked to score more goals in the latter stages of the game.
The 22-year-old striker made an immediate impact as he scored with a thunderous free-kick to make it 4-1 to Pirates, who were running rampant in the dying minutes of the encounter.
Pirates' 5-1 win over Stars was then sealed by Mntambo, whose low shot beat Barra at the near-post in stoppage time much to the delight of the home crowd.
The second-leg encounter will be played in Seychelles next week.
The winner on aggregate between the two teams will face either Namibian side African Stars or Volcan Club of Comoros in the first round.